Digital Commons Network^™

Genome-Wide Identification Of Short 2',3'-Cyclic Phosphate-Containing Rnas And Their Regulation In Aging., Megumi Shigematsu, Keisuke Morichika, Takuya Kawamura, Shozo Honda, Yohei Kirino

Computational Medicine Center Faculty Papers

RNA molecules generated by ribonuclease cleavage sometimes harbor a 2',3'-cyclic phosphate (cP) at their 3'-ends. Those cP-containing RNAs (cP-RNAs) form a hidden layer of transcriptome because standard RNA-seq cannot capture them as a result of cP's prevention of an adapter ligation reaction. Here we provide genome-wide analyses of short cP-RNA transcriptome across multiple mouse tissues. Using cP-RNA-seq that can exclusively sequence cP-RNAs, we identified numerous novel cP-RNA species which are mainly derived from cytoplasmic tRNAs, mRNAs, and rRNAs. Determination of the processing sites of substrate RNAs for cP-RNA generation revealed highly-specific RNA cleavage events between cytidine and adenosine in cP-RNA …

Remodeling Of Chlamydomonas Metabolism Using Synthetic Inducers Results In Lipid Storage During Growth, Nishikant Wase, Boqiang Tu, Girish Kumar Rasineni, Ronald Cerny, Ryan Grove, Jiri Adamec, Paul N. Black, Concetta Dirusso

Department of Biochemistry: Faculty Publications

Microalgae accumulate lipids during stress such as that of nutrient deprivation, concomitant with cessation of growth and depletion of chloroplasts. By contrast, certain small chemical compounds selected by high-throughput screening in Chlamydomonas reinhardtii can induce lipid accumulation during growth, maintaining biomass. Comprehensive pathway analyses using proteomics, transcriptomics, and metabolomics data were acquired from Chlamydomonas cells grown in the presence of one of two structurally distinct lipid activators. WD10784 stimulates both starch and lipid accumulation, whereas WD30030-treated cells accumulate only lipids. The differences in starch accumulation are largely due to differential effects of the two compounds on substrate levels that feed …

Are Proton Pump Inhibitors Among The Risk Factors For Acute Coronary Syndrome?: A Multi-Centric Case-Control Study Between Patients Attending Governmental Hospitals In Western Saudi Arabia, Banan M. Alamoudi, Nahla K. Ibrahim

Saudi Medical Journal

Objectives: To identify the predictors of acute coronary syndrome (ACS) and to determine the relationship between usage of proton pump inhibitors (PPIs) and the occurrence of a first non-fatal ACS event among patients that attended governmental hospitals in Jeddah, Saudi Arabia. Methods: A matched, multi-centric case-control study was performed between January and June of 2015 in Jeddah involving 2 governmental hospitals and the main university hospital. A total of 118 cases aged ≥18 years who were recently diagnosed with ACS were selected. For each case, one control matched by age and gender was selected. Information from an interview questionnaire and …

Middle East Respiratory Syndrome Coronavirus (Mers-Cov) – The Kingdom Of Saudi Arabia

Saudi Medical Journal

No abstract provided.

Spatial And Temporal Variations In Abundance And Composition Of Benthic Macrofauna Associated With Seagrass Beds In Abu Dhabi, Maitha Mohamed Al Hameli

Biology Theses

This study compared the seasonal variations of macrofaunal communities found within the seagrass beds of protected areas and non-protected areas in Abu Dhabi. The study took into consideration the spatial and temporal differences of the sites and seasons as well as other environmental factors, like trace metals concentrations, water temperature, sediment composition, salinity and pH. The main objective and aim of this study is to investigate changes in the community structure of macrofauna with changes in location and seasons. Environmental parameters and biological samples were collected in-situ and analyzed at UAEU labs from both sites, during both seasons (winter and …

Facebook V. Sullivan: Public Figures And Newsworthiness In Online Speech, Thomas E. Kadri, Kate Klonick

Articles

In the United States, there are now two systems to adjudicate disputes about harmful speech. The first is older and more established: the legal system in which judges apply constitutional law to limit tort claims alleging injuries caused by speech. The second is newer and less familiar: the content-moderation system in which platforms like Facebook implement the rules that govern online speech. These platforms are not bound by the First Amendment. But, as it turns out, they rely on many of the tools used by courts to resolve tensions between regulating harmful speech and preserving free expression-particularly the entangled concepts …

The Gut Microbiome Of Freshwater Unionidae Mussels Is Determined By Host Species And Is Selectively Retained From Filtered Seston, Eric A. Weingarten, Carla L. Atkinson, Colin R. Jackson

Faculty and Student Publications

© 2019 Weingarten et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Freshwater mussels are a species-rich group of aquatic invertebrates that are among the most endangered groups of fauna worldwide. As filter-feeders that are constantly exposed to new microbial inoculants, mussels represent an ideal system to investigate the effects of species or the environment on gut microbiome composition. In this study, we examined if host species or site exerts a greater influence …

Vireojd-Mm @ Trecvid 2019: Activities In Extended Video (Actev), Zhijian Hou, Ying-Wei Pan, Ting Yao, Chong-Wah Ngo

Research Collection School Of Computing and Information Systems

In this paper, we describe the system developed for Activities in Extended Video(ActEV) task at TRECVid 2019 [1] and the achieved results. Activities in Extended Video(ActEV): The goal of Activities in Extended Video is to spatially and temporally localize the action instances in a surveillance setting. We have participated in previous ActEV prize challenge. Since the only difference between the two challenges is evaluation metric, we maintain previous pipeline [2] for this challenge. The pipeline has three stages: object detection, tubelet generation and temporal action localization. This time we extend the system for two aspects separately: better object detection and …

Smrtfridge: Iot-Based, User Interaction-Driven Food Item & Quantity Sensing, Amit Sharma, Archan Misra, Vengateswaran Subramaniam, Youngki Lee

Research Collection School Of Computing and Information Systems

We present SmrtFridge, a consumer-grade smart fridge prototype that demonstrates two key capabilities: (a) identify the individual food items that users place in or remove from a fridge, and (b) estimate the residual quantity of food items inside a refrigerated container (opaque or transparent). Notably, both of these inferences are performed unobtrusively, without requiring any explicit user action or tagging of food objects. To achieve these capabilities, SmrtFridge uses a novel interaction-driven, multi-modal sensing pipeline, where Infrared (IR) and RGB video sensing, triggered whenever a user interacts naturally with the fridge, is used to extract a foreground visual image of …

Targeting Parp-1 With Metronomic Therapy As A New Approach To Modulate Mdsc Function And Enhance Anti-Pd1 Immunotherapy In Colon Cancer, Salome Valentina Ibba, Mohamed Ghonim, Abdelmetalab Tarhuni, Matthew Dean, Hamid Boulares, Augusto Ochoa, Youssef Errami, Ali Elbahraway, Ilyes Benslimane, Dorota Wyczechowska, Luis Del Valle, Amir Al-Khami, Hanh Luu

School of Medicine Faculty Publications

34th Annual Meeting and Pre-Conference Programs of the Society for Immunotherapy of Cancer - Part 1, November 6 - 10, 2019, National Harbor, MD

When Players Affect Target Values: Modeling And Solving Dynamic Partially Observable Security Games, Xinrun Wang, Milind Tambe, Branislav Bosanky, Bo An

Research Collection School Of Computing and Information Systems

Most of the current security models assume that the values of targets/areas are static or the changes (if any) are scheduled and known to the defender. Unfortunately, such models are not sufficient for many domains, where actions of the players modify the values of the targets. Examples include wildlife scenarios, where the attacker can increase value of targets by secretly building supporting facilities. To address such security game domains with player-affected values, we first propose DPOS3G, a novel partially observable stochastic Stackelberg game where target values are determined by the players’ actions; the defender can only partially observe these targets’ …

Embryonic Development Of A Parthenogenetic Vertebrate, The Mourning Gecko (Lepidodactylus Lugubris), Aaron H. Griffing, Thomas J. Sanger, Juan D. Daza, Stuart V. Nielsen, Brendan J. Pinto, Edward L. Stanley, Tony Gamble

Biological Sciences Faculty Research and Publications

Background

One goal of evolutionary developmental biology is to understand the role of development in the origin of phenotypic novelty and convergent evolution. Geckos are an ideal system to study this topic, as they are species‐rich and exhibit a suite of diverse morphologies—many of which have independently evolved multiple times within geckos.

Results

We characterized and discretized the embryonic development of Lepidodactylus lugubris—an all‐female, parthenogenetic gecko species. We also used soft‐tissue μCT to characterize the development of the brain and central nervous system, which is difficult to visualize using traditional microscopy techniques. Additionally, we sequenced and assembled a de …

Artificial Intelligence, Finance, And The Law, Tom C.W. Lin

Fordham Law Review

Artificial intelligence is an existential component of modern finance. The progress and promise realized and presented by artificial intelligence in finance has been thus far remarkable. It has made finance cheaper, faster, larger, more accessible, more profitable, and more efficient in many ways. Yet for all the significant progress and promise made possible by financial artificial intelligence, it also presents serious risks and limitations. This Article offers a study of those risks and limitations—the ways artificial intelligence and misunderstandings of it can harm and hinder law, finance, and society. It provides a broad examination of inherent and structural risks and …

Robot, Inc.: Personhood For Autonomous Systems?, Gerhard Wagner

Fordham Law Review

Since the invention of the steam engine, technological progress has served as a driver of innovation for liability systems. Pertinent examples include the arrival of the railway and the introduction of motor-powered vehicles. Today, the digital revolution challenges established legal axioms more fundamentally than technological innovations from earlier times. The development of robots and other digital agents operating with the help of artificial intelligence will transform many, if not all, product markets. It will also blur the distinction between goods and services and call into question the existing allocation of responsibility between manufacturers and suppliers on one side and owners, …

The Due Process And Other Constitutional Rights Of Foreign Nations, Ingrid Wuerth

Fordham Law Review

The rights of foreign states under the U.S. Constitution are becoming more important as the actions of foreign states and foreign state-owned enterprises expand in scope and the legislative protections to which they are entitled contract. Conventional wisdom and lower court cases hold that foreign states are outside our constitutional order and that they are protected neither by separation of powers nor by due process. As a matter of policy, however, it makes little sense to afford litigation-related constitutional protections to foreign corporations and individuals but to deny categorically such protections to foreign states. Careful analysis shows that the conventional …

Design And Modeling Of A New Biomimetic Soft Robotic Jellyfish Using Ipmc-Based Electroactive Polymers, Zakai J. Olsen, Kwang J. Kim

Mechanical Engineering Faculty Research

Smart materials and soft robotics have been seen to be particularly well-suited for developing biomimetic devices and are active fields of research. In this study, the design and modeling of a new biomimetic soft robot is described. Initial work was made in the modeling of a biomimetic robot based on the locomotion and kinematics of jellyfish. Modifications were made to the governing equations for jellyfish locomotion that accounted for geometric differences between biology and the robotic design. In particular, the capability of the model to account for the mass and geometry of the robot design has been added for better …

Long-Term Study On The Population Ecology Of Urban Queen Snakes (Regina Septemvittata) In Central Virginia, Rachel Beiler

Senior Honors Theses

As parts of the world are becoming more urbanized, species living in urban habitat fragments are more at risk of extirpation. We conducted, in an urban environment, a 12-year (2008-2019) mark/recapture study on a Queen snake (Regina septemvittata) population in Rock Castle Creek, Lynchburg, VA to determine population viability. Ninety-nine individual Queen snakes were marked to determine stable population estimates (range 3 - 43 snakes) and an annual survival rate of 52%. Our research found that despite the challenges of urban living, this population is stable and similar to rural Queen snake population studies. Certain life-history traits are …

The Power Of Wording: An Evaluation Of Framing Effects, Chelsea Romph

Honors Capstones

No abstract provided.

The Due Process And Other Constitutional Rights Of Foreign States, Ingrid W. Brunk

Vanderbilt Law School Faculty Publications

The rights offoreign states under the US. Constitution are becoming more important as the actions offoreign states andforeign state-owned enterprises expand in scope and the legislative protections to which they are entitled contract. Conventional wisdom and lower court cases hold that foreign states are outside our constitutional order and that they are protected neither by separation ofpowers nor by due process. As a matter ofpolicy, however, it makes little sense to afford litigation-related constitutional protections to foreign corporations and individuals but to deny categorically such protections to foreign states. Careful analysis shows that the conventional wisdom and lower court cases …

Information Asymmetry And The Protection Of Ordinary Investors, Kevin S. Haeberle

Faculty Publications

To some, the reductions in information asymmetry provided by the main securities-specific disclosure, fraud, and insider-trading laws help ordinary investors in meaningful ways. To others, whatever their larger social value, such reductions do little, if anything for these investors. For decades, these two sides of this investor-protection divide have mostly talked past each other.

This Article builds on economic theory to reveal something striking: The reductions in information asymmetry provided by the core securities laws likely impose a long-overlooked cost on buy-and-hold ordinary investors. More specifically, I explain why there is much reason to believe that the reductions take away …

Property Beyond Exclusion, Lee Anne Fennell

William & Mary Law Review

Property rights have long been associated with a simple and distinctive technology: exclusion. But technologies can become outdated as conditions change, and exclusion is no exception. Recent decades have featured profound changes that have made exclusion a less useful, less necessary, and more expensive way of regulating access to resources. This Article surveys the prospects for a post-exclusion understanding of real and personal property. It proceeds from the premise that property is built upon complementarities, the nature and scale of which have undergone seismic shifts. Physical boundaries and lengthy claims on resources are designed to group complementary elements together in …

Dance Rhythm, Aili W. Bresnahan

Books and Book Chapters by University of Dayton Faculty

This chapter proposes a theory of dance rhythm as distinct from rhythm in dance. First, it distinguishes natural and intentional rhythm, constructed from combining theories by Dewey and Margolis. It then defends this account by exploring musical and non-musical connections between rhythm and dance. It argues that dance rhythm can arise in conjunction with music, or that it can – though need not – follow music, or that it can set the musical rhythm, or be completely independent of music, though natural or internal bodily rhythms can underpin both. Finally, it asserts the existence of dance that might be naturally …

Understanding Nitrogen Limitation In Soybean, Nicolas Cafaro La Menza

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Meeting soybean demand on existing cropland area for a global population of 9.7 billion people by the year 2050 requires narrowing the existing gap between average producer yield and yield potential. Soybean relies on two sources on nitrogen (N): biological N₂ fixation and indigenous soil N supply. As soybean yield continues to increase, it seems critical to know if there is a yield level at which potential contribution of indigenous nitrogen sources and fixation becomes insufficient to meet crop N requirements for high yields, while still maintaining or increasing protein and oil concentration. This study evaluated N limitation across …

Noda-Like Rna Viruses Infecting Caenorhabditis Nematodes: Sympatry, Diversity, And Reassortment, Lise Frézal, Hyeim Jung, Stephen Tahan, David Wang, Marie-Anne Félix

Open Access Publications

Three RNA viruses related to nodaviruses were previously described to naturally infect the nematode

Maternal Fluoxetine Exposure Alters Cortical Hemodynamic And Calcium Response Of Offspring To Somatosensory Stimuli, Rachel M Rahn, Susan E Maloney, Lindsey M Brier, Joseph D Dougherty, Joseph P Culver

Open Access Publications

Epidemiological studies have found an increased incidence of neurodevelopmental disorders in populations prenatally exposed to selective serotonin reuptake inhibitors (SSRIs). Optical imaging provides a minimally invasive way to determine if perinatal SSRI exposure has long-term effects on cortical function. Herein we probed the functional neuroimaging effects of perinatal SSRI exposure in a fluoxetine (FLX)-exposed mouse model. While resting-state homotopic contralateral functional connectivity was unperturbed, the evoked cortical response to forepaw stimulation was altered in FLX mice. The stimulated cortex showed decreased activity for FLX versus controls, by both hemodynamic responses [oxyhemoglobin (HbO

Diffusion Basis Spectrum Imaging For Identifying Pathologies In Ms Subtypes, Afsaneh Shirani, Peng Sun, Kathryn Trinkaus, Dana C Perantie, Ajit George, Robert T Naismith, Robert E Schmidt, Sheng-Kwei Song, Anne H Cross

Open Access Publications

Diffusion basis spectrum imaging (DBSI) combines discrete anisotropic diffusion tensors and the spectrum of isotropic diffusion tensors to model the underlying multiple sclerosis (MS) pathologies. We used clinical MS subtypes as a surrogate of underlying pathologies to assess DBSI as a biomarker of pathology in 55 individuals with MS. Restricted isotropic fraction (reflecting cellularity) and fiber fraction (representing apparent axonal density) were the most important DBSI metrics to classify MS using brain white matter lesions. These DBSI metrics outperformed lesion volume. When analyzing the normal-appearing corpus callosum, the most significant DBSI metrics were fiber fraction, radial diffusivity (reflecting myelination), and …

Human Monoclonal Antibodies Against Chikungunya Virus Target Multiple Distinct Epitopes In The E1 And E2 Glycoproteins, Jose A. Quiroz, Ryan J. Malonis, Larissa B. Thackray, Courtney A. Cohen, Jesper Pallesen, Rohit K. Jangra, Rebecca S. Brown, Daniel Hofmann, Frederick W. Holtsberg, Sergey Shulenin, Elisabeth K. Nyakatura, Lorellin A. Durnell, Vinayak Rayannavar, Johanna P. Daily, Andrew B. Ward, M. Javad Aman, John M. Dye, Kartik Chandran, Michael S. Diamond, Margaret Kielian, Jonathan R. Lai

Open Access Publications

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes persistent arthritis in a subset of human patients. We report the isolation and functional characterization of monoclonal antibodies (mAbs) from two patients infected with CHIKV in the Dominican Republic. Single B cell sorting yielded a panel of 46 human mAbs of diverse germline lineages that targeted epitopes within the E1 or E2 glycoproteins. MAbs that recognized either E1 or E2 proteins exhibited neutralizing activity. Viral escape mutations localized the binding epitopes for two E1 mAbs to sites within domain I or the linker between domains I and III; and for two …

Dc-Script Deficiency Delays Mouse Mammary Gland Development And Branching Morphogenesis, Chunling Tang, Renske J E Van Den Bijgaart, Maaike W G Looman, Nina Tel-Karthaus, Annemarie M A De Graaf, Susan Gilfillan, Marco Colonna, Marleen Ansems, Gosse J Adema

Open Access Publications

Mammary glands are unique organs in which major adaptive changes occur in morphogenesis and development after birth. Breast cancer is the most common cancer and a major cause of mortality in females worldwide. We have previously identified the loss of expression of the transcription regulator DC-SCRIPT (Zfp366) as a prominent prognostic event in estrogen receptor positive breast cancer patients. DC-SCRIPT affects multiple transcriptional events in breast cancer cells, including estrogen and progesterone receptor-mediated transcription, and promotes CDKN2B-related cell cycle arrest. As loss of DC-SCRIPT expression appears an early event in breast cancer development, we here investigated the role of DC-SCRIPT …

Vav1 Inhibits Rankl-Induced Osteoclast Differentiation And Bone Resorption., Jin Sun Jang, In Soon Kang, Young-Nam Cha, Zang Hee Lee, Mary C Dinauer, Young-June Kim, Chaekyun Kim

Open Access Publications

Vav1 is a Rho/Rac guanine nucleotide exchange factor primarily expressed in hematopoietic cells. In this study, we investigated the potential role of Vav1 in osteoclast (OC) differentiation by comparing the ability of bone marrow mononuclear cells (BMMCs) obtained from Vav1-deficient (Vav1-/-) and wild-type (WT) mice to differentiate into mature OCs upon stimulation with macrophage colony stimulating factor and receptor activator of nuclear kappa B ligand in vitro. Our results suggested that Vav1 deficiency promoted the differentiation of BMMCs into OCs, as indicated by the increased expression of tartrate-resistant acid phosphatase, cathepsin K, and calcitonin receptor. Therefore, Vav1 may play a …

Tfeb Activation In Macrophages Attenuates Postmyocardial Infarction Ventricular Dysfunction Independently Of Atg5-Mediated Autophagy, Ali Javaheri, Geetika Bajpai, Antonino Picataggi, Smrithi Mani, Layla Foroughi, Hosannah Evie, Attila Kovacs, Carla J Weinheimer, Krzystztof Hyrc, Qingli Xiao, Andrea Ballabio, Jin-Moo Lee, Scot J Matkovich, Babak Razani, Joel D Schilling, Kory J Lavine, Abhinav Diwan

Open Access Publications

Lysosomes are at the epicenter of cellular processes critical for inflammasome activation in macrophages. Inflammasome activation and IL-1β secretion are implicated in myocardial infarction (MI) and resultant heart failure; however, little is known about how macrophage lysosomes regulate these processes. In mice subjected to cardiac ischemia/reperfusion (IR) injury and humans with ischemic cardiomyopathy, we observed evidence of lysosomal impairment in macrophages. Inducible macrophage-specific overexpression of transcription factor EB (TFEB), a master regulator of lysosome biogenesis (Mϕ-TFEB), attenuated postinfarction remodeling, decreased abundance of proinflammatory macrophages, and reduced levels of myocardial IL-1β compared with controls. Surprisingly, neither inflammasome suppression nor Mϕ-TFEB-mediated attenuation …